A method for generating a velocity-indicating, tomographic image of a sample in an optical coherence tomography system includes the steps of (a) acquiring cross-correlation data from the interferometer; (b) generating a grayscale image from the cross-correlation data indicative of a depth-dependent positions of scatterers in the sample; (c) processing the cross-correlation data to produce a velocity value and location of a moving scatterer in the sample; (d) assigning a color to the velocity value; and (f) merging the color into the grayscale image, at a point in the grayscale image indicative of the moving scatterer's location, to produce a velocity-indicating, tomographic image. Preferably a first color is assigned for a positive velocity value and a second color is assigned for a negative velocity value.